RetrogeneDB ID: retro_fcat_1117

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:118711573..118711901(+)
• Located in intron of: ENSFCAG00000018410

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000006742
• Aliases: None
• Description: None

Sequence

>retro_fcat_1117
CTCCTACAGGCCTCTGAGGAACTGCTAAAGCAGCACCACATTGACATAAAGGCCCACCCATTCTTCCCAGGTCTGCTAAA
GTACCTGAGCTCTGGGCCCATTGTGGCCATGGTTTGGGAGGGTCTGATTGTGGTGAAGACGGGGTGAGTGATGTTTGGGG
AGACCAAACCAGCAGATTGTAAGCCAGGCACCACTCATGAGGACTTCTGTATTCAAGTTGGCAGGAACATCATTCATGGC
AACGATTCAGTAAACAGTGCAGAGAAAGAAATCAGCCTACGGTTTAAACCTAAAGAATTGGTTGACTACAAAGCCTTGTG
CTTTTGAC

Alignment

ORF - retro_fcat_1117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 71.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LIQASEELLKQHYIDLKDRPFFPGLVKYMNSGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFC
          L.QASEELLKQH.ID.K..PFFPGL.KY..SGP.VAMVWEGL.VVKTG.VM.GET.PAD.KPGT...DFC
Retrocopy LLQASEELLKQHHIDIKAHPFFPGLLKYLSSGPIVAMVWEGLIVVKTG*VMFGETKPADCKPGTTHEDFC

Parental  IQVGRNIIHGSDSVKSAEKEISLWFKPEELVDY-KPCAFD
          IQVGRNIIHG.DSV.SAEKEISL.FKP.ELVDY.KPCAFD
Retrocopy IQVGRNIIHGNDSVNSAEKEISLRFKPKELVDY>KPCAFD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	34.20 RPM
SRP017611_kidney	0.00 RPM	64.62 RPM
SRP017611_liver	0.00 RPM	32.65 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1117 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1117 was not experimentally validated.

Homology

Retrocopy orthology:

Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008022	3 retrocopies	retro_amel_1573, retro_amel_390, retro_amel_538,
Bos taurus	ENSBTAG00000047186	1 retrocopy	retro_btau_1329,
Equus caballus	ENSECAG00000021658	1 retrocopy	retro_ecab_404,
Erinaceus europaeus	ENSEEUG00000003783	2 retrocopies	retro_eeur_156, retro_eeur_5,
Felis catus	ENSFCAG00000006742	5 retrocopies	retro_fcat_1083, retro_fcat_1117 , retro_fcat_1475, retro_fcat_216, retro_fcat_663,
Felis catus	ENSFCAG00000008300	3 retrocopies	retro_fcat_1013, retro_fcat_1512, retro_fcat_1672,
Homo sapiens	ENSG00000011052	1 retrocopy	retro_hsap_1063,
Loxodonta africana	ENSLAFG00000007784	1 retrocopy	retro_lafr_636,
Myotis lucifugus	ENSMLUG00000016929	3 retrocopies	retro_mluc_1422, retro_mluc_1882, retro_mluc_637,
Macaca mulatta	ENSMMUG00000001940	1 retrocopy	retro_mmul_1827,
Mustela putorius furo	ENSMPUG00000015573	4 retrocopies	retro_mputfur_1236, retro_mputfur_1590, retro_mputfur_327, retro_mputfur_912,
Mus musculus	ENSMUSG00000020857	1 retrocopy	retro_mmus_221,
Rattus norvegicus	ENSRNOG00000002671	8 retrocopies	retro_rnor_1129, retro_rnor_1610, retro_rnor_1708, retro_rnor_1784, retro_rnor_1966, retro_rnor_2646, retro_rnor_2951, retro_rnor_628,
Sus scrofa	ENSSSCG00000017591	1 retrocopy	retro_sscr_854,
Tupaia belangeri	ENSTBEG00000013053	6 retrocopies	retro_tbel_1271, retro_tbel_1386, retro_tbel_2497, retro_tbel_294, retro_tbel_4620, retro_tbel_820,
Tursiops truncatus	ENSTTRG00000007433	1 retrocopy	retro_ttru_1821,